X-71212113-A-C

Position:

• chrX-71212113-A-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.37 (7386 hom., 9759 hem., cov: 19)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.369 AC: 38960 AN: 105472 Hom.: 7381 Cov.: 19 AF XY: 0.340 AC XY: 9746 AN XY: 28638

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.279

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.338

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.370 AC: 38981 AN: 105492 Hom.: 7386 Cov.: 19 AF XY: 0.340 AC XY: 9759 AN XY: 28670

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.298

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.337

Alfa AF: 0.265 Hom.: 12714

Bravo AF: 0.415

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.65
DANN	Benign	0.42

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7058793; hg19: chrX-70431963;